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Results tagged with samtools
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Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
0
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1
answer
254
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How can I run the latest version of samtools on Slurm?
While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. … /1.11 # this is what I tried first
module spider samtools/1.11 # this does not help either... …
- 579
0
votes
1
answer
356
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How to perform bowtie2 analysis with slurm?
Official manual for bowtie2 says I can use samtools for that. However when I run the following script I have an error
line 22: bowtie2: command not found
Below is the script:
#! … /bash
#SBATCH --time=05:00:00
#SBATCH --account=def-myaccount
#SBATCH --mem=200000M
#SBATCH [email protected]
#SBATCH --mail-type=All
module load nixpkgs/16.09 intel/2018.3
module load samtools …
- 887
1
vote
1
answer
2k
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How can I extract information from .sam files?
I have 10 .sam files after my bowtie2 alignment on ten single-pair sequences. I would like to build a graph based on that output data, however I don't see any other solution but just writing the align …
- 841
3
votes
1
answer
2k
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How to extract unmatched reads using bwa and samtools?
This step uses a combination of bwa mem and samtools view with the parameters –bS –f4. … .fastq format (since this is the format used by the software later)
samtools fastq sample.unmapped.sam > unmatched.fastq
I wonder if these steps are correct? …
M__♦
- 13k
1
vote
1
answer
264
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How can I get unmatched reads for defective genomes analysis using bwa and samtools?
it is required before the analysis)
bwa index sequence.fasta
Then, I have installed samtools
cd ..
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -vxjf samtools … If I got it right - I need this output file to filter with samtools, am I correct? …
2
votes
4
answers
504
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How to make work programs from the $PATH?
/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
sudo tar -vxjf samtools-1.9.tar.bz2
cd samtools-1.9
sudo make
I did not get exactly what does that mean: (must be in your $PATH) but I have … '
I have no idea how samtools must be accessed, I tried sudo command with python3 but it did not work. …
M__♦
- 13k